This is with 1.2.5, but I don't see anything in the changelogs to suggest that this has been addressed.

When verifying a repository, rdiff-backup fails to take hardlinked files into account. (As you know, these files only have the SHA1 digest recorded once in the metadata; the other entries have the inode/device information, but no hash.)

The end result is that some rather confusing (if ultimately harmless) warnings are printed out: